Summary of what happened:
Hi! I’m new to using fMRIprep and am experiencing an error when trying to run an example tutorial. The tutorial I’m following is this one: Using fmriprep for fMRI data preprocessing | by Gelana Tostaeva | Medium. I’ve cloned and copied the entire dataset for the tutorial and I have got the following error when trying to run fMRIPrep. Can anyone figure out what this is all about as I’m a little stuck! Thanks in advance!
Best,
Steve
Command used (and if a helper script was used, a link to the helper script or the command generated):
fmriprep-docker \
/Users/steve/ml_projects/fMRIprep/data/ds000052/ \
/Users/steve/ml_projects/fMRIprep/data/ds000052/output \
participant \
--participant-label 01 \
--fs-license-file /Users/steve/ml_projects/fMRIprep/license.txt
This translates to a call of:
docker run \
--rm \
-e DOCKER_VERSION_8395080871=26.1.4 \
-it \
-v /Users/steve/ml_projects/fMRIprep/license.txt:/opt/freesurfer/license.txt:ro \
-v /Users/steve/ml_projects/fMRIprep/data/ds000052:/data:ro \
-v /Users/steve/ml_projects/fMRIprep/data/ds000052/output:/out \
nipreps/fmriprep:24.0.0 \
/data /out participant \
--participant-label 01
Version:
24.0.0
Environment (Docker, Singularity / Apptainer, custom installation):
Docker
macOs Monterey
Macbook pro (16-inch 2019)
Processor 2,6 Ghz 6-Core intel Core I7
Memory 16 GB 2667 MHz DDR4
Startup Disk Macintosh HD
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
Warning: <8GB of RAM is available within your Docker environment.
Some parts of fMRIPrep may fail to complete.
Continue anyway? [y/N]y
RUNNING: docker run --rm -e DOCKER_VERSION_8395080871=26.1.4 -it -v /Users/steve/ml_projects/fMRIprep/license.txt:/opt/freesurfer/license.txt:ro -v /Users/steve/ml_projects/fMRIprep/data/ds000052:/data:ro -v /Users/steve/ml_projects/fMRIprep/data/ds000052/output:/out nipreps/fmriprep:24.0.0 /data /out participant --participant-label 01
bids-validator@1.14.6
(node:9) Warning: Closing directory handle on garbage collection
(Use `node --trace-warnings ...` to show where the warning was created)
Unhandled rejection (
reason: Error: ENOENT: no such file or directory, scandir '/data/.git/annex/objects/W5'
).
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/bin/fmriprep", line 8, in <module>
sys.exit(main())
^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/fmriprep/cli/run.py", line 40, in main
parse_args()
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/fmriprep/cli/parser.py", line 903, in parse_args
validate_input_dir(
File "/opt/conda/envs/fmriprep/lib/python3.11/site-packages/fmriprep/utils/bids.py", line 245, in validate_input_dir
subprocess.check_call(['bids-validator', str(bids_dir), '-c', temp.name]) # noqa: S607
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/fmriprep/lib/python3.11/subprocess.py", line 413, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['bids-validator', '/data', '-c', '/tmp/tmp_356zewm.json']' returned non-zero exit status 3.
fMRIPrep: Please report errors to https://github.com/nipreps/fmriprep/issues